From b74129e9dc71d61e3bd08e2bddb9d2b6533d852a Mon Sep 17 00:00:00 2001 From: GregJohnsonJr Date: Mon, 10 Mar 2025 14:42:26 -0400 Subject: [PATCH 1/3] Fix for #35 --- R/import_data.R | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/R/import_data.R b/R/import_data.R index 44fff3b..cdb2f67 100644 --- a/R/import_data.R +++ b/R/import_data.R @@ -88,10 +88,27 @@ import_data <- function(peak_table, meta_data, format = "none") { ) mpactr_object <- mpactr$new( - peak_table = df, + peak_table = unique_compounds(df), meta_data = data.table(meta_data) ) mpactr_object$setup() filter_object <- filter_pactr$new(mpactr_object) return(filter_object) } + + +unique_compounds <- function(peak_table_list) { + peak_table <- peak_table_list$peak_table + duplicates <- names(which(table(peak_table$Compound) > 1)) + + for(name in duplicates) { + idx <- which(peak_table$Compound == name) + for(i in seq(length(idx))){ + peak_table$Compound[[idx[[i]]]] <- paste0(peak_table$Compound[[idx[[i]]]], "_", i) + } + } + return(list( + "peak_table" = peak_table, + "raw_table" = peak_table + )) +} From 54c2d7476a6aab955d62777a218e2459df67471a Mon Sep 17 00:00:00 2001 From: GregJohnsonJr Date: Mon, 10 Mar 2025 15:29:29 -0400 Subject: [PATCH 2/3] Added Test data, and new test for the new unique_compounds function. --- R/import_data.R | 5 +- .../testthat/exttestdata/peak_table_dups.csv | 1309 +++++++++++++++++ tests/testthat/test-import_data.R | 16 + 3 files changed, 1329 insertions(+), 1 deletion(-) create mode 100644 tests/testthat/exttestdata/peak_table_dups.csv diff --git a/R/import_data.R b/R/import_data.R index cdb2f67..0b64a7c 100644 --- a/R/import_data.R +++ b/R/import_data.R @@ -100,7 +100,10 @@ import_data <- function(peak_table, meta_data, format = "none") { unique_compounds <- function(peak_table_list) { peak_table <- peak_table_list$peak_table duplicates <- names(which(table(peak_table$Compound) > 1)) - + if(length(duplicates) > 0){ + cli::cli_inform("Found duplicate compound values, will add a suffix to unique + the value.") + } for(name in duplicates) { idx <- which(peak_table$Compound == name) for(i in seq(length(idx))){ diff --git a/tests/testthat/exttestdata/peak_table_dups.csv b/tests/testthat/exttestdata/peak_table_dups.csv new file mode 100644 index 0000000..6f343a5 --- /dev/null +++ b/tests/testthat/exttestdata/peak_table_dups.csv @@ -0,0 +1,1309 @@ +,,,Raw abundance,,,,,,,,,,,,,,,,, +,,,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample,Sample +Compound,m/z,Retention time 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+1332,422.17696,11.45683333,10655.27,5737.01,33477.91,28487.39,11222.92,20043.54,13961.88,9107.94,30362.9,28691.15,11211.29,18412.55,15504.38,8683.32,29340.12,27768.08,11750.24,18710.25 +1333,422.17758,11.45283333,923.77,0,6012.07,4634.47,1250.37,1112.28,1364.87,0,5510.67,4081.4,1096.25,0,1643.83,0,5323.67,4578.46,1073.26,0 +1334,538.39806,11.48116667,1176.19,1353.96,14792.94,3151.34,1590.32,1190.15,1404.99,1636.15,15933.62,2995.29,1350.04,1429.84,982.25,1791.72,16808.92,3039.45,1120.35,1306.39 diff --git a/tests/testthat/test-import_data.R b/tests/testthat/test-import_data.R index 3487413..f21c77a 100644 --- a/tests/testthat/test-import_data.R +++ b/tests/testthat/test-import_data.R @@ -34,3 +34,19 @@ test_that("import_data aborts when expected format = "Progenesis" )) }) + + +test_that("unique_compounds annotate duplicates properly", { + df <- data.frame(Compound = c(1,2,3,1:3,4:7)) + ls <- list(peak_table = df, raw_table = df) + uniqued_list <- unique_compounds(ls) + + expect_true(length(unique(uniqued_list$peak_table$Compound)) == + length(uniqued_list$peak_table$Compound)) + expect_true(length(unique(uniqued_list$raw_table$Compound)) == + length(uniqued_list$raw_table$Compound)) + + expect_false(length(unique(df$Compound)) == length(df$Compound)) +}) + + From 08af3b122269cf4a1e8df53a06daeff2308e84c3 Mon Sep 17 00:00:00 2001 From: YoungKrug Date: Tue, 11 Mar 2025 10:59:26 -0400 Subject: [PATCH 3/3] Making unique duplicates a recursive function. It is possible that adding characters to the end of a compound makes it a non unique compound, this fixes that issue. --- R/import_data.R | 16 +++++++++++++--- tests/testthat/test-import_data.R | 8 ++++++++ 2 files changed, 21 insertions(+), 3 deletions(-) diff --git a/R/import_data.R b/R/import_data.R index 0b64a7c..f215d86 100644 --- a/R/import_data.R +++ b/R/import_data.R @@ -97,12 +97,12 @@ import_data <- function(peak_table, meta_data, format = "none") { } -unique_compounds <- function(peak_table_list) { +unique_compounds <- function(peak_table_list, show_message = TRUE) { peak_table <- peak_table_list$peak_table duplicates <- names(which(table(peak_table$Compound) > 1)) - if(length(duplicates) > 0){ + if(length(duplicates) > 0 && show_message){ cli::cli_inform("Found duplicate compound values, will add a suffix to unique - the value.") + the value.") } for(name in duplicates) { idx <- which(peak_table$Compound == name) @@ -110,6 +110,16 @@ unique_compounds <- function(peak_table_list) { peak_table$Compound[[idx[[i]]]] <- paste0(peak_table$Compound[[idx[[i]]]], "_", i) } } + + # Recursive call to ensure there are no duplicates after fix + duplicates <- names(which(table(peak_table$Compound) > 1)) + + if(length(duplicates) > 0){ + peak_table <- unique_compounds(list( + "peak_table" = peak_table, + "raw_table" = peak_table + ), FALSE)$peak_table + } return(list( "peak_table" = peak_table, "raw_table" = peak_table diff --git a/tests/testthat/test-import_data.R b/tests/testthat/test-import_data.R index f21c77a..40e9cbe 100644 --- a/tests/testthat/test-import_data.R +++ b/tests/testthat/test-import_data.R @@ -47,6 +47,14 @@ test_that("unique_compounds annotate duplicates properly", { length(uniqued_list$raw_table$Compound)) expect_false(length(unique(df$Compound)) == length(df$Compound)) + + df <- data.frame(Compound = c("1", "1", "1_1", "1_1_1")) + ls <- list(peak_table = df, raw_table = df) + uniqued_list <- unique_compounds(ls) + + expect_true(uniqued_list$peak_table$Compound[[4]] == "1_1_1_2") + expect_true(uniqued_list$peak_table$Compound[[1]] == "1_1_1_1") + })